I believe what you want can be indirectly obtained using the function infer.

As in general the actual fitted values from an ARIMA model are of little use themselves, what MATLAB returns is the residuals vector (somewhat oddly). In your case after you have estimated the parameters of the ARIMA model of your choice (model) given your observed univariate time series (data), you can use the model containing the parameter estimates (est) to infer the residuals of your model. So you want something like:

residuals = infer(est,data);

Following that you actual estimated values (est_data) are simply:

est_data = data - residuals;

Take note that infer function uses default setting regarding presample data. I do not know what are R is doing to get its estimates so I would advice you to look at the notion of presample before continuing. You might be surprised about what assumptions are put in place by different packages.

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